It was originally intended to serve the Indian Muslim troops of the British Army stationed at the nearby Whitfield Barracks, now the site of the adjacent Kowloon Park.

In the late 1970s, the building suffered structural issues due to the underground construction carried out for the Mass Transit Railway.

With compensation provided by MTR Corporation and donations from the local Muslim community, a new mosque was built and opened on 11 May 1984 on the present site at 105 Nathan Road to replace the old one.

The most prominent features of the building are the four 11 meters high minarets which mark the corners of the upper terrace and the extensive use of white marble on both the paving and the facade.

There is also a large bus stop situated outside the mosque, with buses to various destinations in Kowloon, New Territories and Hong Kong International Airport.

On 20 October 2019 during the anti-ELAB movement, a Hong Kong Police Force water cannon vehicle filled with stinging blue dye sprayed the Islamic Centre twice.

[10][11][12][13] Masked protesters, pedestrians and mosque-goers rushed to the Islamic Centre to clean up the blue dye left by the police soon after.

[15] Chief Executive Carrie Lam herself came to meet in person with community members and mosque leaders the next day to apologize on the government's behalf over the incident.

A female Senior Superintendent was spotted to not wear a hijab – as required by mosque admission rules – when she entered the Islamic Centre, causing criticism over the faux pas.